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Shin MH, Ku HK, Song JS, Choi S, Son SY, Kim HD, Kim SK, Park IY, Lee SJ. X-ray structure of prephenate dehydratase from Streptococcus mutans. J Microbiol 2014; 52:490-5. [DOI: 10.1007/s12275-014-3645-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/21/2014] [Accepted: 01/27/2014] [Indexed: 10/25/2022]
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Belda E, Sekowska A, Le Fèvre F, Morgat A, Mornico D, Ouzounis C, Vallenet D, Médigue C, Danchin A. An updated metabolic view of the Bacillus subtilis 168 genome. Microbiology (Reading) 2013; 159:757-770. [DOI: 10.1099/mic.0.064691-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Eugeni Belda
- UEVE, Université d'Evry, boulevard François Mitterrand, 91025 Evry, France
- CNRS-UMR 8030, 2 rue Gaston Crémieux, 91057 Evry, France
- CEA, Institut de Génomique, Génoscope Laboratoire d’Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Crémieux, 91057 Evry, France
| | | | - François Le Fèvre
- UEVE, Université d'Evry, boulevard François Mitterrand, 91025 Evry, France
- CNRS-UMR 8030, 2 rue Gaston Crémieux, 91057 Evry, France
- CEA, Institut de Génomique, Génoscope Laboratoire d’Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Anne Morgat
- Swiss Institute of Bioinformatics, CMU, 1 Michel-Servet, CH-1211 Genève 4, Switzerland
| | - Damien Mornico
- UEVE, Université d'Evry, boulevard François Mitterrand, 91025 Evry, France
- CNRS-UMR 8030, 2 rue Gaston Crémieux, 91057 Evry, France
- CEA, Institut de Génomique, Génoscope Laboratoire d’Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Christos Ouzounis
- Department of Biochemistry, Li KaShing Faculty of Medicine, The University of Hong Kong, 21, Sassoon Road, Hong Kong SAR, China
- Institute of Applied Biosciences, Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece
| | - David Vallenet
- UEVE, Université d'Evry, boulevard François Mitterrand, 91025 Evry, France
- CNRS-UMR 8030, 2 rue Gaston Crémieux, 91057 Evry, France
- CEA, Institut de Génomique, Génoscope Laboratoire d’Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Claudine Médigue
- UEVE, Université d'Evry, boulevard François Mitterrand, 91025 Evry, France
- CNRS-UMR 8030, 2 rue Gaston Crémieux, 91057 Evry, France
- CEA, Institut de Génomique, Génoscope Laboratoire d’Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Antoine Danchin
- Department of Biochemistry, Li KaShing Faculty of Medicine, The University of Hong Kong, 21, Sassoon Road, Hong Kong SAR, China
- AMAbiotics SAS, Bldg G1, 2 rue Gaston Crémieux, 91000 Evry, France
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Tan K, Li H, Zhang R, Gu M, Clancy ST, Joachimiak A. Structures of open (R) and close (T) states of prephenate dehydratase (PDT)--implication of allosteric regulation by L-phenylalanine. J Struct Biol 2007; 162:94-107. [PMID: 18171624 DOI: 10.1016/j.jsb.2007.11.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 11/05/2007] [Accepted: 11/09/2007] [Indexed: 11/29/2022]
Abstract
The enzyme prephenate dehydratase (PDT) converts prephenate to phenylpyruvate in L-phenylalanine biosynthesis. PDT is allosterically regulated by L-Phe and other amino acids. We report the first crystal structures of PDT from Staphylococcus aureus in a relaxed (R) state and PDT from Chlorobium tepidum in a tense (T) state. The two enzymes show low sequence identity (27.3%) but the same prototypic architecture and domain organization. Both enzymes are tetramers (dimer of dimers) in crystal and solution while a PDT dimer can be regarded as a basic catalytic unit. The N-terminal PDT domain consists of two similar subdomains with a cleft in between, which hosts the highly conserved active site. In one PDT dimer two clefts are aligned to form an extended active site across the dimer interface. Similarly at the interface two ACT regulatory domains create two highly conserved pockets. Upon binding of the L-Phe inside the pockets, PDT transits from an open to a closed conformation.
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Affiliation(s)
- Kemin Tan
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Building 202, Room A125 9700, S. Cass Avenue, Argonne National Laboratory, Argonne, IL 60439, USA
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Porat I, Waters BW, Teng Q, Whitman WB. Two biosynthetic pathways for aromatic amino acids in the archaeon Methanococcus maripaludis. J Bacteriol 2004; 186:4940-50. [PMID: 15262931 PMCID: PMC451642 DOI: 10.1128/jb.186.15.4940-4950.2004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanococcus maripaludis is a strictly anaerobic, methane-producing archaeon. Aromatic amino acids (AroAAs) are biosynthesized in this autotroph either by the de novo pathway, with chorismate as an intermediate, or by the incorporation of exogenous aryl acids via indolepyruvate oxidoreductase (IOR). In order to evaluate the roles of these pathways, the gene that encodes the third step in the de novo pathway, 3-dehydroquinate dehydratase (DHQ), was deleted. This mutant required all three AroAAs for growth, and no DHQ activity was detectible in cell extracts, compared to 6.0 +/- 0.2 mU mg(-1) in the wild-type extract. The growth requirement for the AroAAs could be fulfilled by the corresponding aryl acids phenylacetate, indoleacetate, and p-hydroxyphenylacetate. The specific incorporation of phenylacetate into phenylalanine by the IOR pathway was demonstrated in vivo by labeling with [1-(13)C]phenylacetate. M. maripaludis has two IOR homologs. A deletion mutant for one of these homologs contained 76, 74, and 42% lower activity for phenylpyruvate, p-hydoxyphenylpyruvate, and indolepyruvate oxidation, respectively, than the wild type. Growth of this mutant in minimal medium was inhibited by the aryl acids, but the AroAAs partially restored growth. Genetic complementation of the IOR mutant also restored much of the wild-type phenotype. Thus, aryl acids appear to regulate the expression or activity of the de novo pathway. The aryl acids did not significantly inhibit the activity of the biosynthetic enzymes chorismate mutase, prephenate dehydratase, and prephenate dehydrogenase in cell extracts, so the inhibition of growth was probably not due to an effect on these enzymes.
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Affiliation(s)
- Iris Porat
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA
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